Hi Luca,
The behavior of the add-in is that it uses the Domino directory to locate mail files homed on the server. It will check all person & mail-in database documents where the server name is the same and scan them. This is so only information about the primary mail file is gathered and not replicas.
The archive scan is slightly different (-r & -R) as it will scan all databases and locate archive databases.
On the servers where no information is gathered I take it that you have mail files homed on the server and email is being delivered to them? The other thing that you may trip you up is that if the mail file design is not based on a standard mail template then the databases will be ignored. You can have a custom mail file template but it must be based on a standard mail template. You can tell if this is the case as the design properties will show something like “StdR9MailCustom is based on StdR9Mail version 9.0.1”.
Let me know how it goes.